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<h2>GENRTF: Generates topology from a Protein Data Bank file</h2><br>

<p>

Genrtf is a program to convert cartesian coordinates into the <a
href="http://www.charmm.org" name="CHARMM">CHARMM</a> input files.
It provides CHARMM input script
with definitions for RTF (CHARMM's Residue Topology File) and template
parameters. It also provides <a href="http://www.rcsb.org"
name"PDB">PDB</a> (Protein Data Bank format) and CRD (CHARMM's
coordinate format), PSF (CHARMM's Protein Structure File) and DCD
(binary trajectory file format) files. DCD is for easier use in <a
href="http://www.ks.uiuc.edu/Research/vmd" name="VMD">VMD</a>
program. Its usage is primarily for easier transformation of PDB files
into CHARMM input script for computer simulations of the biological
systems, but it may be used with other systems as well. It also
generates enough parameters so that HBUILD (automatic build of
coordinates for hydrogens) can be used.

</p>

<p>
genrtf is included in the <a href="http://www.charmming.org">www.charmming.org</a>
</p>

<p>

Input coordinates can be in either XYZ (as produced by <a
href="http://www.cmbi.ru.nl/molden/molden.html" name="MOLDEN">MOLDEN</a>), PDB (default)
or CRD format.

</p>

<p>

If runing ab initio methods with CHARMM, almost no changes are needed
for input file, but it can also help to develop parameters for the
molecules which are not available in the curent CHARMM version.

</p>

<br>
<b>Download</b> <a href="genrtf-2.0.tar.gz" name="genrtf-2.0.tar.gz"><b>genrtf-2.0</b></a><br clear="all">

<br>
<b>Genrtf</b> <a href="http://ala.cmm.ki.si/mailman/listinfo/genrtf" name="genrtf"><b>mailing list</b></a><br clear="all">


<br>
<b>Running genrtf:</b><br clear="all">
<p>
genrtf  [-p] [-a] [-Q] [-q <int>] [-c] [-m] [-x] file
</p>
<p>
-p &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; includes template for parameters<br> 
-a &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; add hydrogens (still needs a lot of work)<br>
-Q &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; add commands to run QM calculation in CHARMM<br>
-q &lt;int&gt; &nbsp;&nbsp; total charge of the system (QM only)<br>
-c&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; input file is in CRD format (CHARMM native)<br>
-x&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; input file is in XYZ format<br>
-m&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;input file is in XYZ format but multiple frames (make movies!)<br>
-19&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;works with MSI topology/parameters
</p>
<p>
By default it reads PDB file format<br>
</p>

NOTE: This documentation is slightly ahaed of the implementations [-m,
-p are only partially implemented]
in the program

<p>
<b>Examples</b>
</p>

<p>
For example one has optimized molecule from <a
href="http://www.gaussian.com">G98</a>, or <a
href="http://www.msg.ameslab.gov/GAMESS/GAMESS.html">GAMESS</a> and wants to make some more
sophisticated restrain minimizations with the CHARMM program:<br>
</p>

<ol>
<li> molden gamess.out<br>
<li> save as XYZ coordinates in the gamess.xyz file<br>
<li> genrtf -q 1 -Q -x gamess.xyz
<li> In the case you want to develop parameters for this system<br>
     charges are already in the CHARMM input script.
</ol>


<p>
Convert CRD coordinates to PDB format without running CHARMM
</p>
<ul>
<li> genrtf -c file.crd
</ul>


<p>
Create complete CHARMM input script with all the necessary files to
run the molecule. It will add hydrogens to the residues which are
specified as HETATM.
</p>

<ul>
<li> genrtf -a 1hbp.pdb
<li> at this stage we have too many hydrogens. (The routine<br>
     which adds them needs some work). One can delete them in the<br>
     coordinate file (1hbp.CRD) and rerun genrtf:
<li> genrtf -c 1hpb.CRD
<li> charmm < 1hpb.i > 1hpb.out
<li> at this stage one has hydrogens on all the atoms build by CHARMM
</ul>

<p>
Create high quality movies: Input file is a bunch of frames in XYZ format,
the same as for MOLDEN. The output is many .atm files which are used
in the movie program. They are converted with the LIGHT program to
.ppm, or some other popular format (like .tga) to make movies with the
Broadcast2000 for example.
</p>

<ul>
<li> genrtf -m anim.xyz
</ul>

movie and LIGHT are separate programs. If there is enough interest
they can be also provided online.


<p>
<b>Bugs</b>
</p>

Do something about if the HETATM atoms have no chain name. Now it says
to many molecules...

CRD does not work now... PDB names for sequence and open statements
don't agree

ala:~/proj/genrtf/examples/2 still does not work. Some atoms have
                             funny names...

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